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8
votes
6
replies
2.1k
views
How do you download from CyVerse using FTP or wget?
cyverse
updated 2.5 years ago by 45k • written 2.5 years ago by ▴ 750
0
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0
replies
1.2k
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Comment: Comment: t2t human reference genome for RNA-seq
2.5 years ago by O.rka ▴ 750
0
votes
2
replies
4.0k
views
Comment: Comment: How could I "recreate" UniRef50/UniRef90 with MMSEQS2?
2.5 years ago by O.rka ▴ 750
1
vote
4
replies
4.0k
views
How could I "recreate" UniRef50/UniRef90 with MMSEQS2?
clustering proteins annotation mmseqs2
updated 2.2 years ago by • 0 • written 2.5 years ago by ▴ 750
1
vote
2
replies
2.4k
views
Are there any tools that can create a very basic GTF file from contig sequences (no annotations really needed) ?
Assembly mapping
2.5 years ago by O.rka ▴ 750
0
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0
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2.4k
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Answer: Answer: Are there any tools that can create a very basic GTF file from contig sequences
2.5 years ago by O.rka ▴ 750
0
votes
0
replies
585
views
What's the state-of-the-art for gene calling in eukaryotic transcriptomics?
modeling eukaryotic transcriptomics call gene
2.6 years ago by O.rka ▴ 750
0
votes
1
reply
2.1k
views
Comment: Comment: How can I run multiple sequence alignment for a large number of proteins (~10k)
2.7 years ago by O.rka ▴ 750
3
votes
5
replies
2.1k
views
How can I run multiple sequence alignment for a large number of proteins (~10k)
muscle msa protein multiple alignment sequence
updated 2.7 years ago by ★ 30k • written 2.7 years ago by ▴ 750
0
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0
replies
2.1k
views
Comment: Comment: How can I run multiple sequence alignment for a large number of proteins (~10k)
2.7 years ago by O.rka ▴ 750
0
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0
replies
2.3k
views
Comment: Comment: Any command line tools that can design primers from a multiple sequence alignmen
2.7 years ago by O.rka ▴ 750
0
votes
1
reply
2.3k
views
Comment: Comment: Any command line tools that can design primers from a multiple sequence alignmen
2.7 years ago by O.rka ▴ 750
0
votes
0
replies
976
views
Comment: Comment: What's best practice when determining a degenerate base when creating a primer?
2.7 years ago by O.rka ▴ 750
1
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2
replies
976
views
What's best practice when determining a degenerate base when creating a primer?
primer-design alignment genomics
2.7 years ago by O.rka ▴ 750
0
votes
1
reply
2.3k
views
Comment: Comment: Any command line tools that can design primers from a multiple sequence alignmen
2.7 years ago by O.rka ▴ 750
1
vote
6
replies
2.3k
views
Any command line tools that can design primers from a multiple sequence alignment?
primer-design genomics cli
2.7 years ago by O.rka ▴ 750
0
votes
1
reply
3.1k
views
Comment: Comment: What in silico PCR commandline tool do you use that can handle IUPAC characters?
2.7 years ago by O.rka ▴ 750
1
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1
reply
3.1k
views
Comment: Comment: What in silico PCR commandline tool do you use that can handle IUPAC characters?
2.7 years ago by O.rka ▴ 750
0
votes
0
replies
84k
views
Comment: Comment: Sequence length from Fasta
2.7 years ago by O.rka ▴ 750
9
votes
6
replies
3.1k
views
What in silico PCR commandline tool do you use that can handle IUPAC characters?
pcr amplicon primer
updated 17 months ago by 45k • written 2.7 years ago by ▴ 750
0
votes
0
replies
1.2k
views
Comment: Comment: How to find full length ribosomal sequences for fungi?
2.7 years ago by O.rka ▴ 750
3
votes
3
replies
1.2k
views
How to find full length ribosomal sequences for fungi?
ncbi ribosomal fungi nt
2.7 years ago by O.rka ▴ 750
0
votes
0
replies
512
views
How to estimate the memory requirements for Diamond given the database and query protein sizes?
alignment diamond memory requirements
2.8 years ago by O.rka ▴ 750
0
votes
0
replies
1.2k
views
Comment: Comment: How to "enrich" a large set of proteins (>11M) for protein hits in UniRef90?
2.8 years ago by O.rka ▴ 750
0
votes
1
reply
1.2k
views
Comment: Comment: How to "enrich" a large set of proteins (>11M) for protein hits in UniRef90?
2.8 years ago by O.rka ▴ 750
0
votes
4
replies
1.2k
views
How to "enrich" a large set of proteins (>11M) for protein hits in UniRef90?
uniref proteins alignment
2.8 years ago by O.rka ▴ 750
0
votes
0
replies
2.1k
views
Comment: Comment: How to extract unmapped reads if you have paired end reads (fastq) and mapped BA
2.9 years ago by O.rka ▴ 750
0
votes
1
reply
2.1k
views
Comment: Comment: How to extract unmapped reads if you have paired end reads (fastq) and mapped BA
2.9 years ago by O.rka ▴ 750
3
votes
4
replies
2.1k
views
How to extract unmapped reads if you have paired end reads (fastq) and mapped BAM file?
fastq bam sam reads
2.9 years ago by O.rka ▴ 750
3
votes
2
replies
1.8k
views
What's the benefit of using the `no_alt_analysis_set` Bowtie2 index over the primary assembly?
human rnaseq mapping metagenomics
updated 2.9 years ago by 89k • written 2.9 years ago by ▴ 750
0
votes
1
reply
915
views
Is there a tool that quantifies “spatial coverage”, that is what percentage of a reference assembly has a read mapped to it?
coverage genomics mapping assembly
updated 3.1 years ago by 153k • written 3.1 years ago by ▴ 750
0
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0
replies
2.9k
views
Comment: Comment: Are there any tools that automatically detect where to truncate forward and reve
3.1 years ago by O.rka ▴ 750
0
votes
0
replies
880
views
Comment: Comment: How to calculate position-specific fastq stats?
3.1 years ago by O.rka ▴ 750
0
votes
2
replies
880
views
How to calculate position-specific fastq stats?
rnaseq fastq metagenomics genomics
3.1 years ago by O.rka ▴ 750
0
votes
3
replies
2.9k
views
Are there any tools that automatically detect where to truncate forward and reverse reads for 16S (DADA2)?
16s dada2 illumina metagenomics qiime2
3.1 years ago by O.rka ▴ 750
0
votes
1
reply
1.9k
views
Comment: Comment: Is it required for all sequences to be same length when clustering OTUs in metag
3.1 years ago by O.rka ▴ 750
1
vote
3
replies
1.9k
views
Is it required for all sequences to be same length when clustering OTUs in metagenomics (ONT Nanopore)
otu metagenomics clustering nanopore
updated 3.1 years ago by 3.4k • written 3.1 years ago by ▴ 750
0
votes
0
replies
975
views
Comment: Comment: What percent identity is recommended for detecting protein homology within a spe
3.1 years ago by O.rka ▴ 750
0
votes
2
replies
975
views
What percent identity is recommended for detecting protein homology within a species?
alignment genomics proteomics
3.1 years ago by O.rka ▴ 750
0
votes
0
replies
3.1k
views
Comment: Comment: Is there a tool that calculates genome coverage? (e.g., 1X, 10X, 100X)
3.2 years ago by O.rka ▴ 750
0
votes
1
reply
3.1k
views
Comment: Comment: Is there a tool that calculates genome coverage? (e.g., 1X, 10X, 100X)
3.2 years ago by O.rka ▴ 750
0
votes
1
reply
3.1k
views
Comment: Comment: Is there a tool that calculates genome coverage? (e.g., 1X, 10X, 100X)
3.2 years ago by O.rka ▴ 750
1
vote
6
replies
3.1k
views
Is there a tool that calculates genome coverage? (e.g., 1X, 10X, 100X)
ncbi metagenomics submission
3.2 years ago by O.rka ▴ 750
0
votes
1
reply
783
views
Software to produce position-specific conservation of multiple sequence alignment results?
transcriptomics genomics alignment proteomics
updated 3.2 years ago by ★ 30k • written 3.2 years ago by ▴ 750
0
votes
1
reply
1.6k
views
How to count the number of multimapped reads from a bam file?
rnaseq mapping bowtie2 featurecounts
updated 3.2 years ago by ★ 1.6k • written 3.2 years ago by ▴ 750
1
vote
1
reply
1.2k
views
Advice on mapping reads to polyploid de-novo assembly
assembly RNA-Seq
updated 3.3 years ago by 7.9k • written 5.6 years ago by ▴ 750
0
votes
1
reply
845
views
How do you predict regions on a protein that are exposed on the cell surface?
protein antibody hmm domain
updated 3.3 years ago by ★ 30k • written 3.3 years ago by ▴ 750
0
votes
0
replies
1.8k
views
Comment: Comment: How can I get a taxid from an assembly id (e.g., GCA_003223415.1 -> 2026742)
3.4 years ago by O.rka ▴ 750
3
votes
2
replies
1.8k
views
How can I get a taxid from an assembly id (e.g., GCA_003223415.1 -> 2026742)
metagenomics accession ncbi taxonomy database
3.4 years ago by O.rka ▴ 750
3
votes
1
reply
1.3k
views
What are the suggested parameters for running IQ-TREE on a protein alignment for phylogeny?
protein metagenomics phylogeny iqtree
updated 3.4 years ago by ★ 30k • written 3.4 years ago by ▴ 750
410 results • Page 2 of 9
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